Windows only: EjectUSB could be considered the nuclear option of USB drives that just won't properly eject in Windows, because there's an "application or process" accessing it. Put EjectUSB on your thumb drive and run it, and the program will mercilessly kill every program, process, or anything else touching your drive, letting you safely remove it without any fear of data loss. It's obviously something you don't want to use when you've got important files open, but it's also a lot more convenient than restarting the computer. EjectUSB is a free download for Windows only; hit the via link below for a command line alternative for Linux systems.